This was happening when I was exporting and importing bindings from a developer machine to our QA (Quality Assurance) environment. Looking back, the problem seems obvious, but it I lost over an hour chasing it down.
So on my developer machine, I had a project reference from the application project to the “BizTalk EDI Application”. On the QA system, I had the same target application, but at that point, it had never used EDI, so it didn’t have the project reference. All I had to do was add the project reference, then the import worked fine.